It seems to be complaining about your faidx file. Check whether ./Reference_Indexed/Human36 is a fasta file and that ./Reference_Indexed/Human36.fai exists and it was made with "samtools faidx" or Picard.
It looks as though something is wrong with the reference sequence specified with --ref

Thank you for the important URL.
in my Parsing indels from CIGAR strings...
"error: faidx error, len==0" appears more than 300,000 times.
And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
Is it normal? Actually I know my sequences have SNPs.

Thank you for the important URL.
in my Parsing indels from CIGAR strings...
"error: faidx error, len==0" appears more than 300,000 times.
And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
Is it normal? Actually I know my sequences have SNPs.